Kidd Lab
Please see complete listing on myNCBI or Google Scholar. Manuscript preprints for many current projects are posted on bioRxiv.
2022
Batcher K, Varney S, York D, Blacksmith M, Kidd JM, Rebhun R, Dickinson P, Bannasch D. Recent, full-length gene retrocopies are common in canids. Genome Res. 2022 Aug 12;32(8):1602–11. PMID: 35961775; PMCID: PMC9435743.
Atindaana E, Kissi-Twum A, Emery S, Burnett C, Pitcher J, Visser M, Kidd JM, Telesnitsky A: Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells. mBio 13(2): e0374821, 2022. PM35384697
Halo JV, Kidd JM: Canis familiaris (Great Dane domestic dog). Trends Genet S0168-9525: 2, 2022. PM35232612
2021
Jagannathan V, Hitte C, Kidd JM, Masterson P, Murphy TD, Emery S, Davis B, Buckley RM, Liu YH, Zhang XQ, Leeb T, Zhang YP, Ostrander EA, Wang GD: Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome. Genes (Basel) 12(6): 847, 2021. PM34070911
Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, Kidd JM: Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proc Natl Acad Sci U S A 118(11): 1-9, 2021. PM33836575/PMC7980453
Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Brain Somatic Mosaicism Network., Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A: Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 22(1): 92, 2021. PM33781308/PMC8006362
2020
Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J: Genomic copy number variation study of nine Macaca species provides new insights into their genetic divergence, adaptation and biomedical application. Genome Biol Evol 12: 2211-2230, 2020. PM32970804
Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C: TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Res 48: e36, 2020. PM32067044
Shen F, Kidd JM: Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. Genes (Basel) 11(2): 141, 2020. PM32013076/PMC7073954
2019
Zhou W, Emery SB, Flash DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE: Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology Nucleic Acids Research, 2019 doi: 10.1093/nar/gkz1173
Kruger AN, Brogley MA, Huizinga JL, Kidd JM, de Rooij DG, Hu YC, Mueller JL: A Neofunctionalized X-Linked Ampliconic Gene Family Is Essential for Male Fertility and Equal Sex Ratio in Mice. Curr Biol. 2019 Oct 9. pii: S0960-9822(19)31107-8
Read DF, Atindaana E, Pyaram K, Yang F, Emery S, Cheong A, Nakama KR, Burnett C, Larragoite ET, Battivelli E, Verdin E, Planelles V, Chang CH, Telesnitsky A, Kidd JM. Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis. PLoS Pathog. 2019 Oct 4;15(10):e1007903
Wang GD, Larson G, Kidd JM, vonHoldt BM, Ostrander EA, Zhang YP: Dog10K: The International Consortium of Canine Genome Sequencing National Science Review nwz068: 1-10, 2019.
Marchant TW, Dietschi E, Rytz U, Schawalder P, Jagannathan V, Hadji Rasouliha S, Gurtner C, Waldvogel AS, Harrington RS, Drögemüller M, Kidd J, Ostrander EA, Warr A, Watson M, Argyle D, Ter Haar G, Clements DN, Leeb T, Schoenebeck JJ. An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome. PLoS Genet 15(5): e1008102, 2019.
Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology. 2019 Mar 7;16(1):6. doi: 10.1186/s12977-019-0468-z.
2018
Larson PA, Moldovan JB, Jasti N, Kidd JM, Beck CR, Moran JV Spliced integrated retrotransposed element (SpIRE) formation in the human genome. PLoS Biol. 2018 Mar 5;16(3):e2003067. doi: 10.1371/journal.pbio.2003067.
Oetjens MT, Martin A, Veeramah KR, Kidd JM Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs BMC Genomics. 2018 May 10;19(1):350. doi: 10.1186/s12864-018-4749-z.
Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol. 2018 Jun 28;16(1):64. doi: 10.1186/s12915-018-0535-2.
featured on BMC On Biology blog
2017
Song S, Sliwerska E, Emery S, Kidd JM Modeling human population separation history using physically phased genomes. Genetics. 2017 DOI: 10.1534/genetics.116.192963. Data available at data dryad
McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 2017 doi: 10.1126/science.aal1641.
Botigué* LR, Song* S, Scheu* A, Gopalan S, Pendleton AL, Oetjens M, Taravella AM, Seregély T, Zeeb-Lanz A, Arbogast RM, Bobo D, Daly K, Unterländer M, Burger J, Kidd JM, Veeramah KR Ancient European dog genomes reveal continuity since the Early Neolithic. Nat Commun. 2017 Jul 18;8:16082. doi: 10.1038/ncomms16082.
featured in the Washington Post
featured in Michigan Radio interview
2016
Henn BM, Botigué LR, Peischl S, Dupanloup I, Lipatov M, Maples BK, Martin AR, Musharoff S, Cann H, Snyder MP, Excoffier L, Kidd JM, Bustamante CD Distance from sub-Saharan Africa predicts mutational load in diverse human genomes Proc Natl Acad Sci U S A 2016 doi: 10.1073/pnas.1510805112
discussed in a perspective by McCoy and Akey
Oetjens MT, Shen F, Emery SB, Zou Z, Kidd JM Y-chromosome structural diversity in the bonobo and chimpanzee lineages. Genome Biol Evol. 2016 Aug 3;8(7):2231-40. PMC4987114 Data available at data dryad.
Zhao X, Emery SB, Myers B, Kidd JM, Mills RE Resolving complex structural genomic rearrangements using a randomized approach. Genome Biol. 2016 Jun 10;17(1):126. PMC4901421
Wildschutte* JH, Williams* ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2326-34 PMC4843416
discussed in a perspective by Jack Lenz
2015
Henn* BM, Botigué* LR, Peischl* S, Dupanloup I, Lipatov M, Maples BK, Martin AR, Musharoff S, Cann H, Snyder MP, Excoffier* L, Kidd* JM, Bustamante* CD. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci U S A. 2015 Dec 28. pii: 201510805 PMC4743782
Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD. The time-scale of recombination rate evolution in great apes. Mol Biol Evol. 2015 Dec 15. pii: msv331.
Wildschutte JH, Baron A, Diroff NM, Kidd JM. Discovery and characterization of Alu repeat sequences via precise local read assembly. Nucleic Acids Res. 2015 Oct 25. pii: gkv1089
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.
1000 Genomes Project Consortium. A global reference for human genetic variation. Nature, 2015 Oct 1;526(7571):68-74
2014
McManus* KF, Kelley* JL, Song* S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Great Ape Genome Project, Kidd# JM, Wall JD, Bustamante CD, Hammer# MF. Inference of gorilla demographic and selective history from whole-genome sequence data. Mol Biol Evol 2014 Dec 21. 21. pii: msu394.
Dayama G, Emery SB, Kidd JM, Mills RE. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Research. 2014 Nov 10;42(20):12640-9. PMC4227756
Martin AR, Costa HA, Lappalainen T, Henn BM, Kidd JM, Yee MC,Grubert F, Cann HM, Snyder M, Montgomery SB, Bustamante CD Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture. PLoS Genet. 2014 Aug 14;10(8):e1004549 PMC4133153
Kidd* JM, Sharpton* TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics. 2014 Apr 4;15(1):262
2013
Auton A, Rui Li Y, Kidd J, Oliveira K, Nadel J, Holloway JK, Hayward JJ, Cohen PE, Greally JM, Wang J, Bustamante CD, Boyko AR Genetic recombination is targeted towards gene promoter regions in dogs. PLoS Genet. 2013 Dec;9(12):e1003984
Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science. 2013 Aug 2;341(6145):562-5.
Prado-Martinez* J, Sudmant* PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. Great ape genetic diversity and population history. Nature. 2013 Jul 3.
2012
1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65.
Casto AM, Henn BM, Kidd JM, Bustamante CD, Feldman MW. A tale of two haplotypes: the EDA2R/AR Intergenic region is the most divergent genomic segment between Africans and East Asians in the human genome. Hum Biol. 2012 Dec;84(6):641-94.
Kidd* JM, Gravel* S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet. 2012 Oct 5;91(4):660-71
Granka JM, Henn BM, Gignoux CR, Kidd JM, Bustamante CD, Feldman MW. Limited Evidence for Classic Selective Sweeps in African Populations. Genetics. 2012 Sep 7
Schoenebeck JJ, Hutchinson SA, Byers A, Beale HC, Carrington B, Faden DL, Rimbault M, Decker B, Kidd JM, Sood R, Boyko AR, Fondon JW 3rd, Wayne RK, Bustamante CD, Ciruna B, Ostrander EA. Variation of BMP3 Contributes to Dog Breed Skull Diversity. PLoS Genet. 2012 Aug;8(8):e1002849
Steinberg* KM, Antonacci* F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE. Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat Genetic. 2012 Jul 1. doi:10.1038/ng.2335
Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M,Gerstein MB, Kidd JM, Bustamante CD, Snyder M Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol. 2012 Mar 7;30(3):226-9
